3DH2 - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH GUANOSINE-3'-CYCLOPHOSPHATE PREPARED BY COCRYSTALLIZATION

Authors :   J. Sevcik, V. Bauerova-Hlinkova

Date :   16 Jun 08 (Deposition) - 16 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Ribonuclease, Hydrolase, Protein-Mononucleotide Complex, Guanosine- 3'-Monophosphate, Mononucleotide, Cocrystallization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Bauerova-Hlinkova, R. Dvorsky, D. Perecko, F. Povazanec, J. Sevci
Structure Of Rnase Sa2 Complexes With Mononucleotides - New Aspects Of Catalytic Reaction And Substrate Recognition
Febs J. V. 276 4156 2009
PubMed-ID: 19558492 | Reference-DOI: 10.1111/J.1742-4658.2009.07125.X

Molecule 1 - RIBONUCLEASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.4.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEH200
	Expression System Strain	:	NOVA BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STREPTOMYCES AUREOFACIENS
	Organism Taxid	:	1894
	Strain	:	R8/26
	Synonym	:	RIBONUCLEASE SA2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	3GP	4	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE
2	BGC	3	Ligand/Ion	BETA-D-GLUCOSE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	3GP	1	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE
2	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	3GP	1	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE
2	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	3GP	1	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE
2	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	3GP	1	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE
2	BGC	-1	Ligand/Ion	BETA-D-GLUCOSE
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:32 , ASN A:33 , ARG A:34 , HOH A:132 , THR C:69 , ASP C:85 , THR D:61 , ARG D:70 , HOH D:101	BINDING SITE FOR RESIDUE BGC A 99
2	AC2	SOFTWARE	PRO B:31 , TYR B:32 , ASN B:33 , ARG B:34 , ARG C:70 , THR D:69	BINDING SITE FOR RESIDUE BGC B 99
3	AC3	SOFTWARE	ARG A:70 , PRO A:84 , HIS A:86 , HOH A:137 , HOH A:140 , TYR C:32 , ASN C:33 , ARG C:34 , ARG C:67	BINDING SITE FOR RESIDUE BGC C 99
4	AC4	SOFTWARE	GLN A:16	BINDING SITE FOR RESIDUE SO4 A 100
5	AC5	SOFTWARE	ARG A:34 , VAL A:37 , PHE A:39 , GLU A:40 , ASN A:41 , ARG A:42 , GLU A:43 , GLU A:56 , ARG A:67 , ARG A:71 , HIS A:86 , TYR A:87 , HOH A:115 , HOH A:123 , ARG C:34 , ARG C:67 , 3GP C:98	BINDING SITE FOR RESIDUE 3GP A 98
6	AC6	SOFTWARE	VAL B:37 , PHE B:39 , GLU B:40 , ASN B:41 , ARG B:42 , GLU B:43 , GLU B:56 , ARG B:67 , ARG B:71 , HIS B:86 , TYR B:87 , HOH B:127 , HOH B:138 , ARG D:34 , ARG D:67 , 3GP D:98	BINDING SITE FOR RESIDUE 3GP B 98
7	AC7	SOFTWARE	GLU A:40 , 3GP A:98 , ARG C:34 , VAL C:38 , PHE C:39 , GLU C:40 , ASN C:41 , ARG C:42 , GLU C:43 , GLU C:56 , ARG C:67 , ARG C:71 , HIS C:86 , TYR C:87	BINDING SITE FOR RESIDUE 3GP C 98
8	AC8	SOFTWARE	3GP B:98 , ARG D:34 , VAL D:37 , VAL D:38 , PHE D:39 , GLU D:40 , ASN D:41 , ARG D:42 , GLU D:43 , GLU D:56 , ARG D:67 , ARG D:71 , HIS D:86 , TYR D:87	BINDING SITE FOR RESIDUE 3GP D 98

Asymmetric Unit

No.	Residues
1	A:9	-	A:97
2	B:9	-	B:97
3	C:9	-	C:97
4	D:9	-	D:97

Asymmetric Unit

No.	Residues
1	Gly A:28	-	Pro A:29
2	Gly B:28	-	Pro B:29
3	Gly C:28	-	Pro C:29
4	Gly D:28	-	Pro D:29

(no "SAP(SNP)/Variant" information available for 3DH2)

(no "PROSITE Motif" information available for 3DH2)

(no "Exon" information available for 3DH2)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:94
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:94
                                    79        89        99       109       119       129       139       149       159    
         Q53752_STRAU    70 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3dh2a_ A: automated matches                                                                   SCOP domains
               CATH domains 3dh2A00 A:4-97  [code=3.10.450.30, no name defined]                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhhh..........eee..............eeeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3dh2 A   4 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    13        23        33        43        53        63        73        83        93

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:94
                                    79        89        99       109       119       129       139       149       159    
         Q53752_STRAU    70 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3dh2b_ B: automated matches                                                                   SCOP domains
               CATH domains 3dh2B00 B:4-97  [code=3.10.450.30, no name defined]                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhhh............................eeeee..........eeeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3dh2 B   4 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    13        23        33        43        53        63        73        83        93

Chain C from PDB  Type:PROTEIN  Length:96
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:96
                                    77        87        97       107       117       127       137       147       157      
         Q53752_STRAU    68 DPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3dh2c_ C: automated matches                                                                     SCOP domains
               CATH domains 3dh2C00 C:2-97  [code=3.10.450.30, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhhh.........ee................eeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3dh2 C   2 DPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    11        21        31        41        51        61        71        81        91

Chain D from PDB  Type:PROTEIN  Length:96
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:96
                                    77        87        97       107       117       127       137       147       157      
         Q53752_STRAU    68 DPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3dh2d_ D: automated matches                                                                     SCOP domains
               CATH domains 3dh2D00 D:2-97  [code=3.10.450.30, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhh..........ee................eeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3dh2 D   2 DPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    11        21        31        41        51        61        71        81        91

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Microbial ribonucleases (174)

Superfamily: Microbial ribonucleases (174)

Family: Bacterial ribonucleases (89)

Protein domain: automated matches (9)

Streptomyces aureofaciens [TaxId: 1894] (8)

1a	d3dh2a_	A:
1b	d3dh2b_	B:
1c	d3dh2c_	C:
1d	d3dh2d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.30, no name defined] (159)

Streptomyces aureofaciens. Organism_taxid: 1894. Strain: r8/26. (4)

1a	3dh2C00	C:2-97
1b	3dh2B00	B:4-97
1c	3dh2D00	D:2-97
1d	3dh2A00	A:4-97

(no "Pfam Domain" information available for 3DH2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q53752_STRAU | Q53752)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:28 - Pro A:29	[ RasMol ]
		Gly B:28 - Pro B:29	[ RasMol ]
		Gly C:28 - Pro C:29	[ RasMol ]
		Gly D:28 - Pro D:29	[ RasMol ]

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	3dh2
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	Q53752_STRAU \| Q53752
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	3.1.4.8
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	Q53752_STRAU \| Q53752	:	1py3 1pyl 3d4a 3d5g 3d5i 3dgy

1gmp	STRUCTURE OF RIBONUCLEASE SA WITH 2'-GMP
1py3	STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
1pyl	STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
3d4a	STRUCTURE OF RIBONUCLEASE SA2 WITH 3'-GMP
3d5i	CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH EXO-2',3'- CYCLOPHOSPHOROTIOATE
3dgy	STRUCTURE OF RIBONUCLEASE SA2 WITH 2'-GMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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SCOP Domains (1, 4)

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